What are Probiotics and How Do They Affect Your Health?

You are here:

What are Probiotics and How Do They Affect Your Health?

What are Probiotics and How Do They Affect Your Health?

Dr. Doni demystifies probiotics: what causes their levels to be altered in the body, what happens when they are disrupted, and how can we get them back on track?

What are Probiotics and How Do They Affect Your Health?“Probiotics” refers to supplements containing bacteria that are good for your gut. The most common bacteria found in probiotic supplements are Lactobacillus acidophilus and bifidobacteria. These are the two most abundant bacteria found in the human intestines, and research indicates that having low levels of these two bacteria increases health risks.

There are actually trillions of micro-organisms living in your intestines, including at least 1,000 different species of bacteria. As a whole, these are referred to as the “microbiome” or “gut microbiota.” They make up an ecosystem within your body, which has only recently been fully studied in the Human Microbiome Project, completed in 2011. We now know that two thirds of your gut microbiota is unique to you, just like your fingerprint.

While we may not like to think of it, and have often heard that we should beware of bacteria, in the case of the bacteria living in our intestines, research indicates that we should be doing everything we can to nurture them. That’s because, in addition to helping with digestion and nutrition, these healthy bacteria turn out to regulate our metabolism (they assist with activating thyroid hormone), appetite, and immune responses. They also prevent invasion by pathogen bacteria (bacteria that are bad for us) and overgrowth of other organisms, such as yeast (read more about yeast here).

In fact, many health issues, including IBS, colitis, reflux, weight gain, diabetes, autoimmunity, asthma, autism, depression, anxiety, and decreased memory have all been shown to be associated with an increase or a decrease in the amounts of these bacteria in the gut.

What happens if we don’t pay attention to these bacteria?

When the balance of healthy bacteria shifts, a ripple effect occurs which can lead to inflammation in the colon, susceptibility to infections, intestinal permeability (or leaky gut), an increased likelihood of reactions to foods such as gluten and dairy, digestive upset (see symptoms below), and issues in other areas of the body, such as rashes, mood changes, weight gain or weight loss.

An imbalance of healthy bacteria, combined with leaky gut, can also increase your risk of diabetes, heart disease, cancer, and neurological conditions (decreased memory or migraines, for example) because the gut and the brain are closely related and problems with one can affect the other.

To learn more about how an imbalanced digestive tract, can become a stress to the body and perpetuate a vicious cycle of unwellness, be sure to read my book, The Stress Remedy. It includes solutions that can help you achieve your health goals.

There are several things that can cause a decrease in our healthy bacteria. These include:

  • Stress and elevated cortisol
  • Antibiotics
  • Infections
  • Anything that disrupts healthy digestion: antacids, proton pump inhibitors, surgery
  • Inflammation, such as from food sensitivities (gluten and others)
  • Heavy metals, pesticides, and toxins
  • Sugar, alcohol, and processed foods
  • Leaky gut

How to tell if your healthy bacteria are too low?

  1. Check your symptoms

If you experience any of these symptoms on a regular basis then your healthy bacteria may be too low:

  • Gas
  • Bloating
  • Changes of bowel movements
  • Burping
  • Stomach and/or abdominal pain
  • Discomfort after eating

Keep in mind, however, that you might not experience any digestive symptoms.

  1. Test the composition of your microbiome

There are tests available that can tell you about the composition of your microbiome. You could either start with a specialized stool panel (different than the standard parasite test) that shows healthy bacteria, as well as unhealthy bacteria, parasites and yeast. This panel will need to be ordered by a naturopathic doctor or holistic/functional practitioner (not available in NY) and I am happy to help (reach my office here). Or you can order a test kit for yourself online at http://ubiome.com.

If you are experiencing nausea and/or the symptoms mentioned above, after seeing a gastroenterologist and potentially having an endoscopy, you might also need to complete a breath test for SIBO (small intestinal bacterial overgrowth), a situation where bacteria become out of balance in the small intestine. You can ask me to help you with this.

What you can do if your healthy bacteria are too low

  1. Add healthy bacteria and address unhealthy microorganisms to your gut by:
  • Taking a high quality probiotic such as Klaire Detoxification Support—read more under “how to find a good probiotic” below. I don’t suggest yogurt as a source because the dairy proteins (casein and whey) and sugar in yogurt negatively affect healthy bacteria.
  • Working with me or another practitioner to address any unhealthy bacteria, parasites, and/or yeast using herbs and natural products.
  • Considering fecal transplantation, which involves introducing healthy stool into your colon in a clinical or home environment.
  1. Manage infections effectively (and hopefully avoid antibiotics) by:
  • Doing your best to prevent infections by eating healthily and optimizing your cortisol levels, as described in The Stress Remedy
  • If you get an infection, work to address it with plenty of sleep, nutrients, herbs and other natural approaches that will hopefully mean you can avoid the use of antibiotics.  Use my Cold/flu Natural Survival Guide or set up an appointment so I can help you.
  • If you do have to take antibiotics, be sure to take a high quality probiotic as well and for at least a month after you stop taking the antibiotics.
  1. Support the ecosystem in your gut every day by:
  • Minimizing or avoiding sugar – which promotes unhealthy bacteria and yeast in your gut.
  • Eating fiber in the form of veggies, fruits, nuts and seeds, and take a prebiotic supplement* such as arabinogalactans (I throw them in my shake each morning).
  • Drinking plenty of water – I suggest 4 to 8 ounces every 2 to 4 hours through the day – which helps to keep your bowel movements regular and your healthy bacteria thriving.
  • Exercising regularly has been associated with a healthier balance of bacteria.
  • Choosing fermented foods (such as sauerkraut, kimchi and pickles) as long as your gut is not aggravated by them.
  • Healing and preventing leaky gut by avoiding foods that trigger inflammation via food sensitivities (such as gluten, dairy, and eggs) as this could disrupt your healthy bacteria
  • Mastering stress and optimizing cortisol levels by identifying what is optimal stress for you and implementing the stress remedies that work best for you. Here is a link to an infographic to help you.

One of the best things you can do, if you think your healthy bacteria need some nurturing, is the Stress Remedy Program (7-day or 21-day). It will help support your internal eco-system by avoiding gluten, dairy, eggs and soy, by choosing organic foods and avoiding sugar and alcohol.

The shake that’s included in the program is not what you might expect from a cleanse shake – it contains organic pea protein with nutrients and enzymes that help heal the digestive tract and stabilize your healthy bacteria.

How to find a good probiotic?

There are many products out there. To find a product vetted by me, check the store at DrDoni.com. I’ve tried many products over the years, and have had varying degrees of success. The products I recommend have resulted in the most positive benefit – and are only available through a practitioner.

While there are some good probiotics available at health food stores, if you don’t see enough positive change, then it is worth investing in a higher quality product.

When choosing a probiotic, look for:

  • Refrigerated bottle (usually okay out of refrigeration for up to 2 weeks)
  • Dairy-free product
  • Expiration date on the bottle
  • Dosing between 5 billion and 100 billion per day

Research indicates that we need more than a good probiotic to resolve a severe bacterial imbalance – so do reach out to me so I can help you if that is your situation. You can click here to make an appointment. Once you start taking a probiotic, as well as a prebiotic, and addressing your stress levels and leaky gut, then you’ll not only feel better each day, but you’ll also be helping to prevent chronic health care concerns in the future.

If you’d like to read about the science behind probiotics, be sure to check out these two articles:

  1. Probiotics, prebiotics, and the host microbiome: the science of translation
  2. Why Antibiotics Are Making Us All Ill – Martin Blaser, The Guardian

Now I’d like to hear from you…

How does it feel to think that we rely on bacteria in our gut to keep us healthy?

Please share your thoughts, and sign up below to receive my next article in your inbox.

Dr Doni
5th June 2014

*Please keep in mind that any and all supplements—nutrients, herbs, enzymes, or other—should be used with caution. My recommendation is that you seek the care of a naturopathic doctor (with a doctorate degree from a federally-accredited program) and that you have a primary care physician or practitioner whom you can contact to help you with individual dosing and protocols. If you ever experience negative symptoms after taking a product, stop taking it immediately and contact your doctor right away.

Share this Post:


  1. Hello Dr. Wilson,

    I have a question about probiotics for you! I currently take them and feel that they help me with my digestion but my husband tells me they make him feel sick… he puts in the terms of “my digestive system feels like it turns off”… can’t say I can relate to that! Anyway, He’s had to take antibiotics a lot in the past (a wrestler all his life, and now very susceptible to bacterial skin infections). We’re having him drink kefir now because the refrigerated bottles probiotics make him feel sick.

    Any suggestions as to why this may be happening??

    Thanks a ton!
    Jaclyn O’Neill

    • Research has taught us so much about probiotics, and we have a lot more to learn. It is not uncommon that one person finds an immediate benefit, while another doesn’t. Especially with that history of antibiotic use, it leads me to think that perhaps his healthy bacteria are imbalanced, and then when he adds in a lot of new good bacteria, the whole environment begins to shift, which can aggravate symptoms. I’d be curious how he is doing with kefir and potentially consider working with a naturopathic doctor who can help him get his whole digestion back to optimal.

  2. Ironically, the link for Klaire probiotic is missing its colon. 😉

    I’m a huge fan of probiotics. They’ve helped my digestion and virtually eliminated smelly gas/excrement. I was taking a really expensive one ($50/month) but I’ve found a $10/month one that works great for me.

    • There are many good probiotics. The key is to know how your healthy bacteria are doing, and then you can use that information to choose an appropriate probiotic for you. The way to find that out is with a stool panel ordered by a naturopathic or functional medicine doctor.

  3. Fantastic article, thank you! I am curious about your thoughts on kefir. I make kefir, kombucha, and fermented vegetables and have some of each daily. I can say that I feel so much better since starting a few months ago. However, kefir is dairy and I know there is a lot of discussion in the health field about whether dairy is good or bad. Also, I have read some articles that question how effective probiotic supplements can be since the acid in the stomach may destroy some of the benefit. Natural probiotics found in foods like kefir are thought to have built in protection against stomach acid. Any thoughts?

    • Hi Sylvia,
      I’m glad you enjoyed the article. One idea for you is to try making kefir in water or other non-dairy liquids. Fermented foods can be a wonderful source of bacteria. I do encourage you to be cautious because I have found that when patients eat fermented foods everyday, they can develop an overgrowth of bacteria. So a little bit of fermented foods can be good, but there is such a thing as too much.

  4. Hi – I was wondering what type of probiotic would you recommend for children ages 1-7 yrs? My son has food allergies and a lot of belly issues. I’m thinking he may have leaky gut by reading some of your articles. Any suggestion on how to build up his immune system because he’s always sick.
    Thanks for your time,

  5. Hi Dr. Doni!

    I wondered if you have heard of Plexus ProBio5? I hear wonderful things about it! It has 5 live strains as well as an anti fungal and is not refrigerated. Thoughts?

Comments are closed.

Master Your Stress, Reset Your Health by Dr. Doni Wilson



Order Now!
More from Dr. Doni

Related Posts

The 5 Burnout Types

Did you know there are 5 burnout types? They are based on your Stress Type®, which is how your adrenal function has been affected by